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Status: Done started: 2020-Apr-01 08:06:23 UTC
Project NameAVP0640
SequenceSTQRRGRTGRGRRGIYR
Secondary structure

CCCCCCCCCCCCCCCCC

Simulation (CABS) temperature3.5 - 1.0
Estimated finish time2020-Apr-01 13:11 UTC

Time evolution of structural features: CABS energy, End-to-end distance and Radius of gyration.

Cluster #123456789
Cluster density63.114.212.511.210.29.08.86.76.6
Cluster size1134541373129261721
Average cluster RMSD1.83.23.33.33.03.23.02.53.2

Clustering of protein models is the task of separating a set of protein models (here a protein dynamics trajectory) into groups (called clusters). The clustering is done in such a way that models are more similar in the same group to each other (here in the sense of RMSD measure), than those in other groups (clusters). CABSfold utilizes classical K-means clustering method.
After clustering is done, each cluster representative is chosen (always the model which average dissimilarity to all models in a cluster is minimal). Predicted protein models, presented in the Predicted structures tab, are each cluster representatives (the clusters and the corresponding models are marked by the same numbers, e.g. Model 1 represents Cluster 1).
The clusters are numbered/ranked according to cluster density values, from the most dense (numbered as a first) to the least dense one.

#123456789
1 0.00 4.81 3.26 4.53 4.68 4.85 5.27 6.31 4.36
2 4.81 0.00 4.73 3.01 5.03 4.94 6.10 7.01 4.45
3 3.26 4.73 0.00 5.45 3.80 3.11 3.28 4.37 4.44
4 4.53 3.01 5.45 0.00 5.02 5.92 6.80 7.90 4.32
5 4.68 5.03 3.80 5.02 0.00 4.47 3.57 4.86 3.70
6 4.85 4.94 3.11 5.92 4.47 0.00 3.29 3.69 5.49
7 5.27 6.10 3.28 6.80 3.57 3.29 0.00 2.74 5.06
8 6.31 7.01 4.37 7.90 4.86 3.69 2.74 0.00 6.62
9 4.36 4.45 4.44 4.32 3.70 5.49 5.06 6.62 0.00

The table contains RMSD values (calculated on the Cα atoms) between the predicted models.
Read more about the root-mean-square deviation (RMSD) measure.

#123456789
1 1.00 0.53 0.68 0.51 0.53 0.53 0.48 0.37 0.48
2 0.53 1.00 0.56 0.63 0.51 0.51 0.51 0.51 0.47
3 0.68 0.56 1.00 0.51 0.59 0.62 0.69 0.56 0.60
4 0.51 0.63 0.51 1.00 0.54 0.44 0.47 0.43 0.54
5 0.53 0.51 0.59 0.54 1.00 0.48 0.62 0.53 0.59
6 0.53 0.51 0.62 0.44 0.48 1.00 0.63 0.63 0.51
7 0.48 0.51 0.69 0.47 0.62 0.63 1.00 0.68 0.51
8 0.37 0.51 0.56 0.43 0.53 0.63 0.68 1.00 0.53
9 0.48 0.47 0.60 0.54 0.59 0.51 0.51 0.53 1.00

The table contains GDT_TS values (calculated on the Cα atoms) between the predicted models.
Read more about the global distance test (GDT, also written as GDT_TS to represent "total score") measure.


 

© Laboratory of Theory of Biopolymers 2013